[phenixbb] Need help in refining my twinned P6322(apparent) dataset

John Pak john.pak at msg.ucsf.edu
Mon Mar 14 23:55:05 PDT 2011

Hey Phenix community,

Here are the details of my current situation - any assistance in the 
matter would be greatly appreciated as I've been struggling mightily for 
the past month trying to get this structure refined (to no avail).


-3.0 angstrom dataset from a membrane protein crystal
-reduced in a P3 Bravis lattice using HKL2000
-Pointless and Xtriage suggest P622 symmetry
-Solved structure via MR - ran Phaser in all P622 based space groups, 
found 1 convincing solution in P6322 (LLG ~110) which makes biological 
sense (1 monomer in ASU that lies on the screw axis to recapitulate the 
biological trimer)
-31% sequence identical search molecule
-no pseudotranslation (via Xtriage)

Xtriage suggests that the P6322 dataset is nearly perfectly twinned 
(twin fraction = 0.49).  Mindful of the fact that there are no twin 
operators for P6322, I'm thinking that the true space group is P321, 
P312 or P63 and I've tried a number of things listed below:

1.  Refined in P6322 (simulated annealing+individual B).  Missing side 
chains and incorrectly modelled loops apparent in maps.  Start R=0.49, 
Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building.

2.  Ran Phaser in P312 (using unrefined model) - no solution.

3. Ran Phaser in P321 (using unrefined model).  One nice solution (LLG 
~220) - lattice looks very similar to P6322 crystal packing.  Twin 
refinement in phenix using operator suggested by Xtriage (simulated 
annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding 

4. Ran Phaser in P63 (using unrefined model).  Three solutions (LLGs all 
~210) - solution #3 looks very similar to P6322 crystal packing.  Twin 
refinement in phenix using operator suggested by Xtriage of solution #3 
gives R=0.37, Rfree=0.40 (no rebuilding performed).  Solutions #1 and #2 
do not give packing arrangements that look like the P6322 solution.  
Twin refinement of Sol 1 and 2 give higher R factors.

So I'm at a loss as to which space group my crystal truly belongs to, 
and where I should be focusing my refinement.  The maps all look similar 
before and after DM.

Thanks for any assistance or recommendations that you might have!

John E. Pak, Ph.D.
Postdoctoral Associate, Stroud Lab
Department of Biochemistry&  Biophysics

Genentech Hall Room S414
600-16th St.
San Francisco, CA 94158-2517

Lab  #:	415-476-3937
Fax  #:	415-476-1902
Cell #:	415-215-0048

More information about the phenixbb mailing list